Discussion: meetings/2025-07-01

[jeromelecoq]

This thread will contain discussion related to the meeting on 2025-07-01.
Agenda :
1 Severine will present Neuropixel targetting strategy.
2 Nicholas will present statistical power analysis
3.Jerome will introduce finalized stimulus design of next experiment

[jeromelecoq]

I will cover this update design :
After updates :
https://docs.google.com/presentation/d/1WFPHhe7XP8DtXoCHj_VGkGm4ukBfVv69UaC4gMWOlio/edit?usp=sharing

Which was translated in code here : https://github.com/AllenNeuralDynamics/openscope-community-predictive-processing/blob/main/code/stimulus-control/src/Standard_oddball_slap2_version2.bonsai

[severine2305]

Sev's presentation on targeting
ImplantHistoryP3Summary.pptx

[maierav]

Suggestion: Place 4-shank Neuropixels in V1 (rather than in the frontal lobe)

Pros:
1 - V1 has the most pronounced columnar organization, and this layout lends itself to studying that
2 - This layout allows for the computation of 3D CSD (see: Leski, Szymon, et al. Neuroinformatics 5.4 (2007): 207-222.), but this will require pronounced responses/high SNR, which is most expected for V1 given visual stimuli

Potential Cons:
The fact that the electrodes are angled poses some theoretical challenges above, but there are good reasons that this is negligible in practice (e.g., CSD seems to work and make sense under these conditions).

V1 may show the least oddball response modulation.

[severine2305]

Hi everyone, I would like to discuss further the 4 shanks in V1. Currently we have only NP 1.0 on the rig. And we have never done experiments with different types of probes. Here are listed as many pros as cons for the 4 shanks. I asked people in Allen who are using different types of probes in 1 experiment about downstream consequences (sorting, data conversion, annotations and area labeling), and I was told it is not plug and play and will require work. I would like to have your opinion on what is the most valuable approach here and if the 4 shank will indeed add precious scientific value. As I mention last week my main con is that 4 insertions on a 4 shank in the same hole and same angle will be very difficult to annotate (and decide where are the V1 channels). Please let me know what you think!

[Dedalus9]

Presentation on orientation tuning vector variability; preliminary analysis for statistical power analysis. Will expand on this power point in this thread and later include a link to a GoogleColab for this statistical analysis.
Oweiss_Lab_Nicholas_Rodriguez_7_1_Presentation.pptx

[farznaj]

my summary nots on coordinates

PL: prelimbic cortex (PL; a subregion of the mPFC) *
AP +2.68 mm,
ML 0.5 mm,
subpial (SP) 0.85 mm.
For Ca2+ imaging of PL neurons projecting to the ACC, 0.1 μL of retrograde AAV encoding FLP (AAVrg-EF1a-FLPo; 55637; Addgene) was injected into the left
Also check:
Selective engagement of prefrontal VIP neurons in reversal learning
They use 1.8mm for prelimbic, and pretty deep!!
ACC:
AP +0.75 mm,
ML 0.5 mm,
SP 1 mm
and 0.1 μL of FLP-dependent GCaMP6s (AAV8-EF1a-fDIO-GCaMP6s; 105714; Addgene) was injected into the left PL of C57BL/6 mice.
Thy1-GCaMP6s mice were utilized for imaging pyramidal neurons in the PL and the ACC in combination with chemogenetic manipulation.
Activation of VIP interneurons in the prefrontal cortex ameliorates neuropathic pain aversiveness - ScienceDirect

Rafael Yuste:
ACa:
600 anterior from bregma
−300 lateral
−900 μm deep
V1:
Y = 200 from lambda
X = −2,500 lateral
Z = −250 μm deep
Cortical ensembles selective for context | PNAS

Jordan Hamm Cell Reports paper:
Aca (Anterior Cingulate Area):
Y = 1.98 mm, from bregma (but he thinks it's a typo, and should have been 0.98mm; see email below).
Y = 0.98 mm
X = 0.35 mm
V1:
Y = −2.92 mm
X = 2 mm
[Frontiers | Lack of functional specialization of neurons in the mouse primary visual cortex that have expressed calretinin](https://www.frontiersin.org/articles/10.3389/fnana.2014.00089/full

[farznaj]

[severine2305]

Thank you so much!